Protein aggregation is mediated by short aggregation-prone sequences that assemble into intermolecular beta-structures, which form the core of the aggregate. In native conditions, these stretches are buried inside the globular structure of the protein and are, hence, protected from aggregation by the thermodynamic stability of the fold. Although the vast majority of proteins contain at least one such aggregation-prone region, protein aggregation in healthy cells is effectively suppressed by a number of mechanisms, which cooperate to maintain proteostasis (Balch, Morimoto et al. 2008). One of them are gatekeeper residues, strongly enriched at the flanks of the aggregating regions, that slow down the aggregation reaction (Otzen, Kristensen et al. 2000; Richardson and Richardson 2002; Rousseau, Serrano et al. 2006; Monsellier and Chiti 2007). Moreover, molecular chaperones, such as Hsp70, bind to exposed aggregating regions, preventing intermolecular assembly to nucleate (Van Durme, Maurer-Stroh et al. 2009). Finally, protein turnover rates (De Baets, Reumers et al. 2011) and protein expression levels (Tartaglia, Pechmann et al. 2009) are tuned to minimize problems with protein aggregation. During normal ageing, these cellular defense mechanisms have been shown to erode (Kikis, Gidalevitz et al. 2010) and many proteins have been observed to break through the proteostasis boundary in ageing tissues (Lee, Weindruch et al. 2000; Zou, Meadows et al. 2000; Lund, Tedesco et al. 2002; Pletcher, Macdonald et al. 2002; Lu, Pan et al. 2004; Ben-Zvi, Miller et al. 2009; Bishop, Lu et al. 2010), often without apparent adverse effects. On the other hand, aggregation of specific proteins has been convincingly linked to a number of age-related human diseases, including neurodegenerative disorders such as Alzheimer Disease and Parkinson Disease, as well as cancer (Xu, Reumers et al. 2011) and metabolic diseases (Ishii, Kase et al. 1996; Soong, Brender et al. 2009). In these cases, the aggregation problem is often exacerbated through mutations, which increase the solvent exposure of the aggregation-prone regions by thermodynamically destabilizing the native structure (Dobson 2004).
However, when proteins are employed for research, therapy or industrial applications, they need to withstand artificial conditions for which evolution has poorly equipped them. Given the ubiquitous nature of aggregation-prone sequences in the proteome, it is not surprising that protein aggregation is often observed when proteins are expressed far beyond their normal concentration in conditions with insufficient or no molecular chaperones. Moreover, once purified, the proteins are expected to last far beyond their natural lifetime, allowing the critical nucleating events to start the protein aggregation reaction. Several methods have been developed to reduce the aggregation problem, for example, by using cell lines with increased chaperone content (Schlieker, Bukau et al. 2002), by generating fusion proteins with solubilizing tags (Zhang, Howitt et al. 2004; Park, Han et al. 2008; Song, Lee et al. 2011), or by careful formulation of buffers (Wang 1999). Another approach would be to adapt the primary sequence to the new requirements through carefully selected mutations. Although this approach has the disadvantage of altering the protein sequence, this is often not a prohibitive consideration.